Rapid identification of health threatening bacteria and/or spores present in small concentration in sample fluids is of utmost importance. Efficient sample preparation and molecular detection aims to achieving this goal. Two processes must be conducted successively: the concentration of the targets in a small volume with simultaneous purification, followed by their lysis to provide accessible DNA templates. Conventional PCR is then used in situ to identify the targets. In this work we present an original approach combining an efficient concentration and purification of the bacteria and spores, a rapid and efficient grinding lysis step, working even for polluted samples, and the integration of the process in a semi-automated device. The method is very efficient and rapid: it can concentrate and detect less than 10 targets in 1 mL of sample, even if the sample is contaminated by some environmental contaminants. The most resistant spores are successfully lysed. In this study, we successively present the principle and performances of the method, and its integration on a in a semi-automated device. Perspectives to fully integrated system are discussed. © 2017 Elsevier B.V.